By browsing the code on Bitbucket it appears you can simply override the default compton conf by dropping yours in ~/.config/marco-compton.conf
Here are the relevant lines from the source:
# Allow users to override the defaults by creating their own config
# for this wrapper.
if [ -f ${HOME}/.config/${WM}-compton.conf ]; then
compton \
--config ${HOME}/.config/${WM}-compton.conf &
else
compton \ [...]
Cheers